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Genomic Science Program

2009 Awardee

Phenomic Analysis of Natural and Induced Variation in Brachypodium distachyon

INVESTIGATORS: J.P. Vogel, M. Watt, R.T. Furbank, H. Budak, and M. Tuna

INSTITUTION: USDA-ARS Western Regional Research Center

NON-TECHNICAL SUMMARY: Herbaceous energy crops, especially grasses, are poised to become a major source of energy in the United States. Despite their increasing importance, we know little about the basic biology underlying the traits that control the utility of grasses as energy crops. Better knowledge of basic grass biology (e.g., identification of the genes that control cell-wall composition, plant architecture, cell size, cell division, reproduction, nutrient uptake, carbon flux, etc.) could be used to design rational strategies for crop improvement and shorten the time required to domesticate these new crops. We propose to conduct high-throughput phenotypic analysis (phenomics) of homozygous T-DNA mutants and natural accessions of the model grass Brachypodium distachyon ( Brachypodium ) to accelerate the acquisition of this knowledge.

OBJECTIVES: (1) Assemble a collection of natural accessions and 2,000 homozygous T-DNA lines. (2) Conduct a detailed phenotypic characterization of the collection using a phenomic approach. (3) Begin detailed characterization of a select group of mutants and natural accessions.

APPROACH: Obj. 1. Through a previous Feedstock Genomics grant, we have already assembled a collection of over 4,000 T-DNA lines and are generating 100 additional lines per week. For the present study, we will identify 2,000 lines homozygous for their respective T-DNA insertions. Natural variation is another rich source of diversity, and we have assembled a collection of over 200 diverse accessions, primarily from Turkey. Based on genotypic data from genetic markers, we will select 100 inbred lines for phenomic characterization.

Obj. 2. Accurate phenotypic characterization of large numbers of individuals under carefully controlled conditions is a costly and rate-limiting step for functional genomic projects. These analyses typically involve destructive measurements, multiple replicate sets of plants, and exhaustive manual labor. An additional problem is that measurements made at different times on different sets of plants are not directly comparable due to small variations in environmental conditions. The “phenomic” approach to these problems is to perform multiple non-destructive phenotypic measurements in an automated high-throughput fashion on a large number of plants at one time and, where possible, make repeated observations over time to provide more robust data. We will use this approach to fully characterize the phenotype of T-DNA mutants and inbred lines under defined environmental conditions.

Obj. 3. To relate the phenotypic data to the function of individual genes requires detailed molecular-genetic characterization. To begin this process, we will select a small group of mutants and natural accessions for detailed characterization aimed at identifying and verifying the genes responsible for particular phenotypes. While much of this work will extend beyond the term of the current proposal, our T-DNA resources will greatly accelerate this process.

Name: J.P. Vogel
Phone: 510-559-6117
Fax: 510-559-5818


Funding Announcement DE-FOA-0001865:
Systems Biology of Bioenergy-Relevant Microbes to Enable Production of Next-Generation Biofuels and Bioproducts.
Pre-App required 01/08/2018, 5 PM Eastern [12/17]



Biosystems Design to Enable Next-Generation Biofuels (Summary of Funded Projects) [12/17]

Technologies for Characterizing Molecular and Cellular Systems Relevant to Bioenergy and Environment [9/17]

ASCR BER Exascale Requirements Review [9/17]


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